Molecular dynamics modeling of tubulin C-terminal tail interactions with the microtubule surface

Tubulin, an alpha/beta heterodimer, has had most of its 3D structure analyzed; however, the carboxy (C)-termini remain elusive. Importantly, the C-termini play critical roles in regulating microtubule structure and function. They are sites of most of the post-translational modifications of tubulin and interaction sites with molecular motors and microtubule-associated proteins. Simulated annealing was used in our molecular dynamics modeling to predict the interactions of the C-terminal tails with the tubulin dimer. We examined differences in their flexibility, interactions with the body of tubulin, and the existence of structural motifs. We found that the alpha-tubulin tail interacts with the H11 helix of beta-tubulin, and the beta-tubulin tail interacts with the H11 helix of alpha-tubulin. Tail domains and H10/B9 loops interact with each other and compete for interactions with positively-charged residues of the H11 helix on the neighboring monomer. In a simulation in which alpha-tubulin's H10/B9 loop switches on sub-nanosecond intervals between interactions with the C-terminal tail of alpha-tubulin and the H11 helix of beta-tubulin, the intermediate domain of alpha-tubulin showed more fluctuations compared to those in the other simulations, indicating that tail domains may cause shifts in the position of this domain. This suggests that C-termini may affect the conformation of the tubulin dimer which may explain their essential function in microtubule formation and effects on ligand binding to microtubules. Our modeling also provides evidence for a disordered-helical/ helical double-state system of the T3/H3 region of the microtubule, which could be linked to depolymerization following GTP hydrolysis.